kassonlab/brer-md issues and pull requests

#63 - Include version information in log output

Issue - State: open - Opened by eirrgang over 1 year ago

#62 - Restore RunData from state.json

Pull Request - State: closed - Opened by eirrgang over 1 year ago - 1 comment

#61 - State file not restored.

Issue - State: closed - Opened by eirrgang over 1 year ago

#60 - MANIFEST.in needs more tweaking

Issue - State: open - Opened by eirrgang over 1 year ago

#59 - Include conftest.py in the sdist.

Pull Request - State: closed - Opened by eirrgang over 1 year ago

#58 - conftest.py needs to be added to the distribution archives

Issue - State: closed - Opened by eirrgang over 1 year ago - 2 comments
Labels: bug

#57 - Further improve import error reporting.

Pull Request - State: closed - Opened by eirrgang over 1 year ago - 2 comments

#56 - Better reporting for import errors.

Pull Request - State: closed - Opened by eirrgang over 1 year ago

#55 - Log the actual import error.

Issue - State: closed - Opened by eirrgang over 1 year ago

#54 - Test mult-rank simulator.

Pull Request - State: open - Opened by eirrgang over 1 year ago

#53 - Tighten pytest compatibilty.

Pull Request - State: closed - Opened by eirrgang over 1 year ago

#52 - Support MPI-GROMACS

Pull Request - State: closed - Opened by eirrgang over 1 year ago - 1 comment

#51 - Remove RDMAV_FORK_SAFE override.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago

#50 - Limit the scope of mpi4py.MPI dependency.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago - 1 comment

#49 - Allow manually triggering the GitHub Actions workflows.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago - 1 comment

#48 - Expand test coverage.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago

#47 - Consider suppressing or delaying MPI initialization.

Issue - State: closed - Opened by eirrgang almost 2 years ago - 1 comment

#46 - Address libfabric complaint about `fork()`.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago

#45 - Error with GitHub Actions environment and libfabric

Issue - State: closed - Opened by eirrgang almost 2 years ago
Labels: bug

#44 - Use updated pybind11 for older gmxapi installations.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago

#43 - Patch GROMACS 2019.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago

#42 - Trained parameters are not loaded from state file.

Issue - State: open - Opened by eirrgang almost 2 years ago
Labels: bug

#41 - Simplify build infrastructure

Issue - State: open - Opened by eirrgang almost 2 years ago - 1 comment
Labels: Priority::Low

#40 - Clarify pybind11 version

Pull Request - State: closed - Opened by eirrgang almost 2 years ago

#39 - Harden the path search for gmxapi CMake config.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago - 1 comment

#38 - Logic error in CMAKE_PREFIX_PATH handling

Issue - State: closed - Opened by eirrgang almost 2 years ago
Labels: bug

#37 - Update GitHub Action versions and workflow syntax.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago

#36 - Normalize and disambiguate handling of name field.

Pull Request - State: closed - Opened by eirrgang almost 2 years ago - 1 comment

#35 - Inconsistent handling of name field wrt pair data.

Issue - State: closed - Opened by eirrgang almost 2 years ago - 1 comment

#34 - Register the project and add classification metadata.

Issue - State: open - Opened by eirrgang almost 2 years ago
Labels: documentation, good first issue

#33 - Add a CITATION.cff file.

Issue - State: open - Opened by eirrgang almost 2 years ago
Labels: documentation, good first issue

#32 - Add overlooked dependencies.

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 1 comment

#31 - Use more recent pybind11

Issue - State: closed - Opened by eirrgang about 2 years ago

#30 - Minor tidying to README.rst

Pull Request - State: closed - Opened by eirrgang about 2 years ago
Labels: documentation

#29 - Pair names don't match when WorkElement is used.

Issue - State: open - Opened by eirrgang about 2 years ago - 1 comment
Labels: good first issue, question

#28 - Minor docs clean-up.

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 1 comment
Labels: documentation

#27 - Update docs for plugin potential parameters.

Issue - State: open - Opened by eirrgang about 2 years ago
Labels: documentation, good first issue

#26 - Update ensemble initializaton.

Issue - State: open - Opened by eirrgang about 2 years ago

#25 - utility functions to collect the paths of prev_state files for completed iterations.

Issue - State: open - Opened by eirrgang about 2 years ago

#24 - Establish/maintain RunData state at a higher level.

Issue - State: open - Opened by eirrgang about 2 years ago

#23 - Record the simulation input for each iteration and phase.

Issue - State: open - Opened by eirrgang about 2 years ago

#21 - Outdated issue links in comments

Issue - State: open - Opened by eirrgang about 2 years ago
Labels: good first issue

#20 - Finish simplifying data structures.

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 4 comments

#19 - Normalize and clarify ensemble_num default.

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 1 comment

#18 - Add a compatibility utility module.

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 1 comment

#17 - Update conf.py

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 1 comment

#16 - Docs build updates

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 1 comment

#15 - Documentation improvements.

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 3 comments

#14 - Refactor remaining MetaData subclasses.

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 1 comment

#13 - Update GitHub Actions

Issue - State: closed - Opened by eirrgang about 2 years ago
Labels: good first issue

#12 - Refactor PluginConfig classes

Pull Request - State: closed - Opened by eirrgang about 2 years ago

#11 - Missing test coverage.

Issue - State: open - Opened by eirrgang about 2 years ago
Labels: good first issue

#10 - Update internal data structures.

Issue - State: closed - Opened by eirrgang about 2 years ago - 2 comments

#9 - pair_data.json file needs documentation

Issue - State: closed - Opened by eirrgang about 2 years ago - 3 comments

#8 - Update appearance (formatting) in API docs.

Issue - State: closed - Opened by eirrgang over 2 years ago
Labels: good first issue

#7 - Ensemble workflow management and MPI compatibility

Issue - State: open - Opened by eirrgang about 2 years ago

#6 - Clarify support for (re)sampling from a pool of starting conformations.

Issue - State: closed - Opened by eirrgang over 2 years ago - 11 comments

#5 - Need updated logic for better behavior under `mpiexec`

Issue - State: open - Opened by eirrgang about 2 years ago

#4 - Linting, etc.

Issue - State: open - Opened by eirrgang about 2 years ago
Labels: good first issue

#3 - Clean up the way parameter structures are expressed in C++.

Issue - State: open - Opened by eirrgang about 2 years ago

#2 - Update documentation.

Pull Request - State: closed - Opened by eirrgang about 2 years ago - 2 comments

#1 - Fix logic error in build backend.

Pull Request - State: closed - Opened by eirrgang about 2 years ago

GitHub / kassonlab/brer-md issues and pull requests